Since the first report of a clinical strain in England in 1961, methicillin-resistant Staphylococcus aureus (MRSA) has become one of the principal pathogenic bacteria of nosocomial infection. It poses a major healthcare concern due to the high morbidity and mortality in patients associated with hospital and community acquired infections. MRSA bacterium is a variant of Staphylococcus aureus that has acquired drug resistance to β-lactam antibiotics such as methicillin, oxacillin, and ampicillin by the integration of a transposon known as Staphylococcal Cassette Chromosome (SCC). Antibiotic resistance is reported to be associated with the acquisition of penicillin-binding protein 2a (PBP2a) by Staphylococcus aureus. PBP2a purportedly has a lower affinity to β-lactam antibiotics. In 2009, Contreras-Martel et al. described single nucleotide polymorphisms (SNPs) in a Streptococcus pneumoniae penicillin binding protein (pbp) gene ultimately leading to decreased susceptibility to beta-lactam antibiotics. This is different from what is normally seen in Staphylococcus aureus, in which PBP2a is an alternate penicillin binding protein acquired form the environment that exhibits lower beta-lactam binding affinity.
There are four (4) predominant SCC types of MRSA; namely, type I, type II, type III and type IV MRSA. Types I-III are hospital-associated MRSA (HA-MRSA) and type IV is community-associated MRSA (CA-MRSA). CA-MRSA is associated with the Panton-Valentine leukocidin (PVL) toxin and represents a highly virulent type of MRSA. Risk of Staphylococcus aureus infection is high for patients who have opened wounds or weakened immune systems staying in hospitals and nursing homes, as well as for other healthcare facilities. Once an individual is infected with MRSA, the choice of effective antibiotics is limited. These include alternate antibiotics (e.g., vancomycin and teicoplanin and linezolid). Therefore, accurate MRSA identification and SCC typing of the microorganism is crucial and there is a continuing need for an accurate and speedy identification of MRSA. Early detection of various types of MRSA constitutes an important determinant for the treatment of MRSA-infected patients.
Current methodology in detecting and typing MRSA predominantly involves use of molecular PCR technology. In 1986, Matsuhashi et al. cloned the mecA gene that encodes an alternative penicillin binding protein, pbp2a. The mecA gene is known to exist on SCC of MRSA and coagulase-negative Staphylococci (MRC-NS), but not on methicillin-susceptible Staphylococcus aureus (MSSA). The mecA gene is therefore considered a gene adventitiously acquired in the genomes of Staphylococcus aureus. Detection of the mecA gene in the genomic DNA of Staphylococcus aureus generally is achieved by PCR (polymerase chain reaction) or hybridization, which makes it possible to identify it as either MRSA or MRC-NS. However, identification of MRSA using this mecA detection method suffers from the following problems. First, direct detection of the mecA gene from a sample, even if successful, cannot be taken as a proof of the existence of MRSA. Second, this method requires culturing of the bacterial strain from a patient's sample and confirmation of Staphylococcus aureus by a conventional strain identification method. These conventional strain identification methods require a minimum of 48-72 hours to provide a positive MRSA identification. Doctors often are reluctant to provide an empiric therapy until an infectious strain is identified.
Single nucleotide polymorphism (SNP) is a common form of genetic polymorphism. SNPs may influence gene functions and modify a microorganism's ability to manifest a disease process. Although it is generally understood that a disease often has a genetic component in its etiology and may be unraveled in genetic association studies, to date and to the best of the present inventors' knowledge, there are no reported genetic markers (e.g., SNPs) that are associated with methicillin-resistant Staphylococcus aureus (MRSA), let alone one of the most virulent MRSA (i.e., community-associated MRSA).
Accordingly, there is a need for a genetic marker to predict the presence of CA-MRSA. The need for such a reliable SNP biomarker for CA-MRSA is believed to have utility in the bacteriology application in the detection of MRSA. The present inventors cured all the prior art deficiency and discovered specific SNPs that are useful in predicting the presence of CA-MRSA.